The web app can't control which application is used to open the file on the client. It just provides the MIME type, and then the user gets to choose the application. For PDFs, most often that will be Acrobat, but it could also be something like Preview (on OS X). If the file has features only Acrobat supports (like filling in forms),
you should mention that next to the download link.
You can't control what happens after the viewing app is closed. The user may have switched to other applications in the mean time anyway, and will get back to the web app when it's convenient to her. What is the purpose of wanting to control this?
